Cell state · L2
MG.baseline
2,106 cells in the full atlas (not the displayed sample).
These are the cell-population annotations shown in the SCREATE Cell Browser.
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Marker genes
CSF1R, CX3CR1, HEXB, ITGB5, OLFML3, P2RY12, SALL1, SELPLG, TMEM119, TREM2
Annotation genes
CX3CR1, P2RY12, TMEM119, TREM2
Annotation rationales
A core homeostatic microglial identity is evident: P2RY12 (purinergic ATP/ADP sensor) and TMEM119 are signature markers of parenchymal microglia that distinguish them from infiltrating macrophages; CX3CR1 mediates tonic neuron–microglia communication via neuronal CX3CL1, maintaining a quiescent, surveillant state with fine ramified processes; TREM2, together with CSF1R, supports survival, lipid sensing, and basal phagocytic tone required for constant synaptic/aptotic-body clearance. SALL1 enforces the microglial transcriptional program and HEXB/ITGB5/OLFML3 reflect lysosomal and matrix-interaction readiness appropriate for synaptic niche maintenance.
Functional implications
Continuous, non-inflammatory surveillance of the CNS: patrol synapses, sample extracellular ATP/ADP via P2RY12, and adjust microglial motility/morphology through CX3CR1 signaling to preserve circuit function. Perform low-level phagocytosis and lipid handling (via TREM2) to clear apoptotic debris and prune weak synapses, thereby supporting learning-dependent synaptic remodeling without triggering damaging inflammation.
Marker and functional descriptions are atlas annotations. Explore gene expression, trait associations and regulatory elements in the interactive browsers; see the browser guide.